Recurrent Mutations Research Articles

Targeting Epigenetic Dysregulations in Head and Neck Squamous Cell Carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is one of the deadliest human cancers, with the overall 5-year survival rate stagnating in recent decades due to the lack of innovative treatment approaches. Apart from the recently Food and Drug Administration-approved epidermal growth factor receptor inhibitor and immune checkpoint inhibitor, alternative therapeutic strategies that target epigenetic abnormalities, an emerging cancer hallmark, remain to be fully explored. A pathological epigenetic landscape, characterized by widespread reprogramming of chromatin modifications such as DNA methylation and histone modifications, which drives transcription deregulation and genome reorganization, has been extensively documented in numerous cancers, including HNSCC. Growing evidence indicates that these frequent epigenomic alterations play pivotal roles in regulating malignant transformation, promoting metastasis and invasion, and reshaping the tumor microenvironment. Furthermore, these epigenetic changes also present unique vulnerabilities that open new avenues for identifying novel prognostic biomarkers and developing targeted antitumor therapies. In this review, we summarize recent discoveries of epigenetic dysregulations in HNSCC, with a focus on deregulated chromatin modifications, which include aberrant DNA methylation, oncohistone H3 lysine 36 to methionine (H3K36M) mutation, as well as recurrent mutations or altered expression of chromatin-modifying enzymes such as NSD1, EZH2, and KMT2C/D. Importantly, we discuss the various molecular mechanisms underlying the contributions of these epigenetic alterations to HNSCC development, particularly their involvement in deregulated cell proliferation and cell death, metabolic reprogramming, tumor immune evasion, and phenotypic plasticity. Finally, we conclude by highlighting the translational and clinical implications of targeting the epigenetic machinery, which offers promising prospects for overcoming resistance to conventional radiotherapy/chemotherapy and enhancing the response to immunotherapy in HNSCC.

Molecular and immune landscape of hepatocellular carcinoma for therapeutic development.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide, with an estimated 750,000 deaths in 2022. Recent emergence of molecular targeted agents (MTAs) and immune checkpoint inhibitors (ICIs) and their combination therapies have been transforming HCC care, but their prognostic impact in advanced-stage disease remains unsatisfactory. In addition, their application to early-stage disease is still an unmet need. Omics profiling studies have elucidated recurrent and heterogeneously present molecular aberrations involved in pro-cancer tumor (immune) microenvironment that may guide therapeutic strategies. Recurrent aberrations such somatic mutations in TERT promoter and TP53 have been regarded undruggable, but recent studies have suggested that these may serve as new classes of therapeutic targets. HCC markers such as alpha-fetoprotein (AFP), glypican-3 (GPC3), and epithelial cell adhesion molecule (EpCAM) have also been explored as therapeutic targets. These molecular features may be utilized as biomarkers to guide the application of new approaches as companion biomarkers to maximize therapeutic benefits in patients who are likely to benefit from the therapies, while minimizing unnecessary harm in patients who will not respond. The explosive number of new agents in the pipelines have posed challenges in their clinical testing. Novel clinical trial designs guided by predictive biomarkers have been proposed to enable their efficient and cost-effective evaluation. These new developments collectively facilitate clinical translation of personalized molecular-targeted therapies in HCC and substantially improve prognosis of HCC patients.

Pharmacological inhibition of ezrin reduces proliferative and invasive phenotype in acute lymphoblastic leukemia cells

Ezrin (EZR) is an actin-associated protein that is often upregulated in cancers. Here we investigate the role of EZR in acute lymphoblastic leukemia (ALL) and explore the therapeutic potential of a pharmacological EZR inhibitor, NSC305787. ALL patient cohorts exhibit significantly elevated EZR mRNA levels, indicating its association with the malignant phenotype. Notably, EZR expression does not impact survival outcomes or relevant clinical-laboratory characteristics, suggesting a role in disease initiation rather than therapy response. NSC305787 induces a dose-dependent reduction in ALL cell viability, and is more potent than a related EZR inhibitor, NSC668394. NSC305787 has multiple effects on ALL cells, including apoptosis induction, clonal growth reduction, and inhibition of cell cycle progression. Importantly, it diminishes adhesiveness and invasiveness in ALL cells. Proteomics analysis highlights changes in translation, RNA catabolism, and cell cycle regulation, emphasizing the broad impact of EZR inhibition on ALL cell biology. Ex vivo assays with primary cells from acute myeloid leukemia (AML) and ALL patients demonstrate NSC305787's efficacy across a molecularly heterogeneous group, independent of risk stratification or recurrent mutations. Notably, NSC305787 shows heightened potency in ALL cells, suggesting its potential as a targeted therapy. In conclusion, our results report high EZR expression in adult ALL patients and support NSC305787 as a promising targeted therapy for ALL that should be further explored.

The molecular landscape of 227 adult granulosa cell tumors of the ovary: Insights into the progression from primary to recurrence

Adult granulosa cell tumors (AGCTs) of the ovary are characterized by their propensity for late recurrences and are primarily managed surgically due to the limited efficacy of systemic treatment. The FOXL2 p.C134W somatic mutation has been identified in ∼95% of AGCT cases, and TERT promoter alterations have been linked to worse overall survival. This study highlights the potential prognostic significance of FOXO1 mutations, suggesting that they may be associated with poorer overall survival and shorter time to recurrence. A total of 183 primary AGCTs and 44 recurrences without corresponding primary tumors were analyzed. The primary AGCTs were categorized into three groups: 77 non-recurrent tumors, 18 tumors which later recurred (including 9 cases with matched primary-recurrence pairs), and 88 tumors with unknown recurrence status. Targeted next-generation sequencing was conducted on 786 cancer-related genes to investigate their genetic profile. The study aimed to identify the molecular alterations associated with AGCT pathogenesis and recurrence rate, comparing primary vs. recurrent tumors, and primary-recurrent vs. primary non-recurrent cases. Our findings confirmed the high prevalence (99%) of the FOXL2 p.C134W mutation in AGCTs. Secondary truncating FOXL2 mutations were observed in 5% of cases. Two cases with typical AGCT morphology were FOXL2 wild-type, harboring mutations in KRAS or KMT2D instead, suggesting alternative genetic pathways. TERT promoter mutations were found in 43% of cases, more frequently in recurrences. Other recurrent mutations detected in the cohort included KMT2D (10%), FOXO1 (7%), CHEK2 (5%), TP53 (3.5%), PIK3CA (3.5%), and AKT1 (3%). Two recurrent, FOXL2-mutated cases also carried DICER1 mutations. One tumor exhibited MSI-High status and a TMB of 19 mut/Mb. Our results indicate the need for further investigation into the role of FOXO1 as a potential prognostic marker in AGCTs.

Clinical Utility of a Novel Triplex Digital PCR Assay for Clone Monitoring in Sequential and Relapsed Pediatric B-Cell Acute Lymphoblastic Leukemia Patients.

Digital polymerase chain reaction (PCR) studies for clonal disease monitoring in B-acute lymphoblastic leukemia patients are currently limited due to the heterogeneous nature of mutations, which limit cost-effective assay designs. In this study, 70 samples (14 relapse and 56 sequential therapy samples) were tested for 13 recurrent mutations identified on deep sequencing in our published cohort (KRAS, NRAS, NT5C2, PMS2, UHRF1, KMT2D, and TP53 genes) via a novel triplex digital PCR assay. A total of seven major clones of NRAS [five] and NT5C2 [two] were noted in six out of 14 (43%) relapse patients, accounting for 44% of early relapses. In addition, 10 minor clones (PMS2 [two], NRAS [four], NT5C2 [three], and TP53 [one]) were noted in five out of 14 (36%) patients. In the 56 sequential therapy samples, six major clones were noted (NRAS [five], KRAS [one]) in four out of 14 (28.5%) patients, with two increasing in size in maintenance samples, leading to subsequent relapse in both cases. In addition, therapy-acquired minor clones in NT5C2 [four] and PMS2 [one] were seen to emerge in maintenance samples in four out of 14 (28.5%) patients, with concordant detection of such major and minor clones in unpaired relapse samples, indicating the need for their active surveillance during therapy. Overall, digital PCR validated NRAS and NT5C2 major clones in one-third (10 out of 27; 37%) of cases, driving nearly half of early relapses.

Cutaneous hybrid cysts with matrical differentiation are mostly sporadic and related to CTNNB1 mutation.

Recurrent mutations in the CTNNB1 or APC genes leading to the activation of the Wnt/betacatenin pathway are observed in adnexal tumors with matrical differentiation. While most pilomatricomas arise sporadically and harbor CTNNB1 mutations, cutaneous hybrid cysts combining epidermal and matrical differentiations have been mostly reported in a context of the familial adenomatosis polyposis/Gardner's syndrome related to germinal mutations of APC. The objective of this study is to understand the pathogenesis of hybrid cysts combining epidermal and matrical differentiations. The 287 cases diagnosed as pilomatricoma/hybrid cysts registered between January 1, 2015 and February 21, 2023 in the Pathology Department at Tours University Hospital Center were considered for inclusion. After diagnosis confirmation, all cases were classified as pilomatricomas or hybrid cysts. Clinical data and microscopic features of the two groups were compared. Immunohistochemical detection of the betacatenin and CTNNB1/APC genes sequencing were performed in all hybrid cysts. Among the cohort, ten cases were classified as hybrid cysts (4%). None had a personal or familial history of familial adenomatosis polyposis. The immunochemistry confirmed a betacatenin nuclear expression in the matrical component in allexcepted one cases, while no nuclear accumulation was observed in the epidermal component of most hybrid cysts (n = 8, 80%). CTNNB1 mutations were detected in all hybrid cysts with interpretable sequencing data (n = 7/10). By contrast, only a variant of uncertain significance (class 3) was detected in APC in association with a pathogenic CTNNB1 mutation in one case. Hybrid cysts are rare entities consisting in 4% of the tumors analyzed in our study. Our results suggest that most hybrid cysts occur sporadically and are associated with CTNNB1 somatic mutations.

Emergence of carbapenem resistance in persistent Shewanella algae bacteremia: the role of pdsS G547W mutation in adaptive subpopulation dynamics

This study elucidates the in vivo genetic mechanisms contributing to the emerging resistance to carbapenem in Shewanella algae through a lens of adaptive microbial evolution. Leveraging PacBio amplification-free sequencing, we tracked the evolution of β-lactam resistance in clinical isolates from a persistent S. algae bacteremia case amidst antimicrobial therapy. Our investigation spotlighted a recurrent G547W mutation in the sensor histidine kinase (pdsS), which was associated with the overexpression of an OmpA-like protein (pdsO) within a proteobacteria-specific sortase system. Intriguingly, we observed a recurrent switch between wild-type and G547W alleles, revealing an adaptive expansion and contraction of underlying cell subpopulations in response to β-lactam exposure. Comparative transcriptome analyses further demonstrated the overexpression of genes pivotal for membrane integrity, biofilm formation, immune evasion, and β-lactamase activation in resistant samples. This underscores the pre-existence of resistant cells at minuscule frequencies even without antibiotic pressure, potentially explaining the within-host emergence of resistance during antibiotic treatments. Our findings provide pivotal insights into the dynamic genetic adaptations of S. algae under therapeutic pressures, unmasking intricate resistance mechanisms and highlighting the critical role of subpopulation dynamics in treatment outcomes.

Mechanistic basis of atypical TERT promoter mutations

Non-coding mutations in the TERT promoter (TERTp), typically at one of two bases −124 and −146 bp upstream of the start codon, are among the most prevalent driver mutations in human cancer. Several additional recurrent TERTp mutations have been reported but their functions and origins remain largely unexplained. Here, we show that atypical TERTp mutations arise secondary to canonical TERTp mutations in a two-step process. Canonical TERTp mutations create de novo binding sites for ETS family transcription factors that induce favourable conditions for DNA damage formation by UV light, thus creating a hotspot effect but only after a first mutational hit. In agreement, atypical TERTp mutations co-occur with canonical driver mutations in large cancer cohorts and arise subclonally specifically on the TERTp driver mutant chromosome homolog of melanoma cells treated with UV light in vitro. Our study gives an in-depth view of TERTp mutations in cancer and provides a mechanistic explanation for atypical TERTp mutations.

High-grade B-cell lymphoma not otherwise specified, with diffuse large B-cell lymphoma gene expression signatures: Genomic analysis and potential therapeutics.

High-grade B-cell lymphoma not otherwise specified (HGBCL, NOS) has overlapping morphological and genetic features with diffuse large B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL), leading to uncertainty in its diagnosis and clinical management. Using functional genomic approaches, we previously characterized HGBCL and NOS, that demonstrate gene expression profiling (GEP), and genetic signatures similar to BL. Herein, we characterize distinct HGBCL, NOS, cohort (n = 55) in adults (n = 45) and in children (n = 10), and compared the GEP, genomic DNA copy number (CN), and mutational spectrum with de novo DLBCL (n = 85) and BL (n = 52). This subgroup, representing ~60% of HGBCL, NOS, lack gene-expression signature of BL and double hit/dark zone lymphoma, but express DLBCL like signatures and are characterized by either GCB- or ABC-like mRNA signatures and exhibit higher genomic complexity, similar to de novo DLBCL, and show alteration in genes regulating B-cell activation (CD79B, MYD88, PRDM1, TBLIXR1, CARD11), epigenome (KMT2D, TET2) and cell cycle transition (TP53, ASPM). However, recurrent mutations in genes often mutated in BL (DDX3X, GNA13, CCND3), but rare in DLBCL, are also present in HGBCL-NOS, highlighting genetic heterogeneity. Consistent with mutation spectrum, frequent genomic CN alterations in genes regulating B-cell activation (del-PRDM1, gain-BCL6, -REL, -STAT3) and cell cycle regulators (del-TP53, del-CDKN2A, del-RB1, gain-CCND3) were observed. Pediatric cases showed GCB-DLBCL-like mRNA signatures, but also featured hallmark mutations of pediatric BL. Frequent oncogenic PIM1 mutations were present in adult HGBCL, NOS. In vitro analyses with pharmacologic or genetic inhibition of PIM1 expression triggered B-cell activation and NF-κB-induced apoptosis, suggesting that PIM1 is a rational therapeutic target.

Mutant PP2A Induces IGFBP2 Secretion to Promote Development of High-Grade Uterine Cancer.

Uterine serous carcinoma (USC) and uterine carcinosarcoma (UCS) tumors are uniquely aggressive, suggesting that the primary tumor is intrinsically equipped to disseminate and metastasize. Previous work identified mutational hotspots within PPP2R1A, which encodes the Aα scaffolding subunit of protein phosphatase 2A (PP2A), a heterotrimeric serine/threonine phosphatase. Two recurrent heterozygous PPP2R1A mutations, P179R and S256F, occur exclusively within high-grade subtypes of uterine cancer and can drive tumorigenesis and metastasis. Elucidation of the mechanisms by which PP2A-Aα mutants promote tumor development and progression could help identify therapeutic opportunities. Here, we showed that expression of these mutants in USC/UCS cell-lines enhanced tumor-initiating capacity, drove a hybrid epithelial-to-mesenchymal (EM) plasticity phenotype, and elevated secretion of the tumorigenic cytokine IGFBP2. Therapeutic targeting of the IGFBP2/IGF1R signaling axis using small molecules and genetic approaches resulted in marked tumor growth inhibition. Mechanistically, PP2A regulated IGFBP2 expression through the transcription factor, NF-κB, which harbors a B56 recognition motif. Collectively, these results identify a role for PP2A in regulating paracrine cancer cell signaling that can be targeted to block the initiation and metastasis of high-grade uterine cancer.

EPCO-35. GENOMIC CHARACTERIZATION OF GROWTH HORMONE SECRETING PITUITARY ADENOMAS

Abstract BACKGROUND Pituitary adenomas (PAs) are the second most common brain tumors in adults with prevalence ranging from 80 to 100 per 100,000 individuals. Of these, 9% to 14% are growth hormone (GH)-secreting PAs. While recurrent somatic GNAS mutations are identified in approximately half of sporadic GH-secreting PAs, the remaining cases are not well-characterized. This study aims to expand the genomic profile of GH-secreting PAs and explore correlations between molecular and clinical features. METHODS Whole exome sequencing (WES) was performed on 19 tumors with matching blood samples from consenting patients, achieving mean coverages of 262.74X for tumor samples and 112.43X for blood samples. Somatic variants, including single nucleotide variants (SNVs), short insertions/deletions (INDELs), and copy number variations (CNVs), were identified, and analyzed using protocols established by our institution. Genomic instability was assessed by calculating the percentage of the genome displaying loss-of-heterozygosity (LOH). Clinical data were collected and analyzed to establish genomic correlations. RESULTS The cohort comprised 19 GH-secreting PAs, with a mean age of 46 years at surgery, and was predominantly female (78.9%). The cohort was enriched for macroadenomas, with a mean tumor size of 18.4 mm. WES revealed a mean somatic mutation count of 20.4 (range 7-79), with 47% of cases harboring recurrent GNAS mutations. The mean alteration by LOH across the cohort was 11.13% (range: 0-44.80%) and did not show a statistically significant difference between cases with GNAS mutations and GNAS-wildtype cases (7.71% vs. 14.21%, respectively). Chromosomes 3, 8, 16, 22q were frequently affected by CNV/LOH events. CONCLUSION Comprehensive genomic characterization, including assessment of genomic instability through CNV/LOH analysis, is critical for better understanding the pathogenesis of GH-secreting PAs. This study underscores the importance of detailed genomic profiling in larger cohorts for improving the diagnosis and management of these tumors.

EPCO-41. THE NUCLEOSOME REMODELING AND DEACETYLASE COMPLEX UNDERLIES SELECTIVE DEPENDENCY IN H3 G34-MUTANT DIFFUSE HEMISPHERIC GLIOMA

Abstract Pediatric-type diffuse high-grade gliomas are fatal central nervous system malignancies of childhood. Recurrent mutations in histone H3.3 at amino acid 34 (glycine to arginine/valine) are a defining molecular feature of diffuse hemispheric glioma, H3 G34-mutant (H3 G34-mutant DHG), which arises preferentially in adolescents and young adults. Single-nuclei sequencing of age and anatomically matched H3 wild-type and H3 G34-mutant primary patient tumors identified aberrant neuronal-like transcriptional programs enriched for signatures of cortical interneurons derived from the medial ganglionic eminence. The extent to which these molecular signatures reflect cancer dependencies in H3 G34-mutant DHG is poorly understood. To identify transcriptional vulnerabilities governing cellular state and underlying developmental lineage, we performed CRISPR screening targeting the DNA-binding domains of 1,427 proteins in H3 G34-mutant DHG (n=6) and H3 K27-altered diffuse midline glioma (DMG) (n=3). Through these efforts, we identified developmentally relevant transcription factor vulnerabilities corresponding to neuronal and oligodendrocyte precursor cell-like hierarchies comprising H3 G34-mutant DHG and H3 K27-altered DMG cellular states, respectively. Intriguingly, we also identified multiple members of the nucleosome remodeling and deacetylase (NuRD) complex as selective dependencies in H3 G34-DHG compared to H3 K27-altered DMG and 32 other cancer cell line models screened using the same DNA-binding domain library. Genetic perturbation of the holo-NuRD structural subunit MBD3 conferred an upregulation of genes involved in neuronal differentiation and synapse formation consistent with NuRD-mediated modulation of the aberrant neuronal-like cell hierarchy observed in H3 G34-mutant DHG. To therapeutically target NuRD-associated class I HDAC activity, patient-derived H3 G34-mutant DHG cell lines were treated with quisinostat, a highly potent class I and II HDAC inhibitor. Pharmacologic inhibition of HDAC activity was sufficient to impair cell growth in vitro. Ongoing experiments are evaluating dependencies in vivo. Our results may suggest a differential requirement for chromatin repressive complex dysregulation in the pathogenesis of oncohistone-mutant pediatric-type diffuse high-grade gliomas.

CSIG-26. TARGETING EPIGENETIC DYSREGULATION AND ADAPTIVE RESISTANCE MECHANISMS IN DIPG/DMG

Abstract Diffuse intrinsic pontine gliomas (DIPG/DMG) are devastating pediatric brain tumors with very limited treatment options and a uniformly fatal prognosis. The recurrent histone H3K27M mutation in DIPG disrupts epigenetic regulation, leading to the hypothesis that this mutation-induced dysregulation creates a vulnerability to epigenetic targeting. We conducted a screening of compounds targeting epigenetic enzymes to identify potential inhibitors of patient-derived DIPG cell growth. High-throughput screening identified chaetocin, a fungal metabolite, as a potent inhibitor of DIPG cell growth. Chaetocin treatment selectively decreased proliferation and increased apoptosis in DIPG cells, significantly extending survival in DIPG xenograft models while restoring H3K27me3 levels. The loss of the H3K9 methyltransferase SUV39H1 also inhibited DIPG cell growth. Transcriptomic and epigenomic profiling showed that SUV39H1 loss or inhibition downregulated stemness and oncogenic networks, including growth factor receptor signaling. However, D2 dopamine receptor (DRD2) signaling adaptively upregulated, conferring resistance. Combining chaetocin with the DRD2 antagonist ONC201 or radiotherapy synergistically enhanced antitumor efficacy. This study reveals a therapeutic vulnerability in DIPG cells by targeting the SUV39H1-H3K9me3 pathway and compensatory signaling loops. Combining SUV39H1-targeting chaetocin with other agents, such as ONC201, may offer a new strategy for effective DIPG treatment. The findings suggest that chaetocin, by targeting and suppressing the H3K9me3 methyltransferase SUV39H1, inhibits DIPG tumor growth by downregulating stemness-related genes and growth factor signaling pathways. Overall, the study highlights a new therapeutic vulnerability in DIPG through the SUV39H1-H3K9me3 epigenetic pathway and compensatory signaling loops, suggesting an effective treatment strategy for DIPG.

EPCO-17. CARM1 METHYLATES GLIOBLASTOMA TUMOR SUPPRESSOR QUAKING TO REGULATE ITS TRANSCRIPTIONAL COACTIVATOR FUNCTION

Abstract Glioblastoma (GBM) represents the most prevalent and deadly primary brain tumor in adults, and it remains highly refractory to current therapeutic interventions. Significant intratumor heterogeneity drives rapid invasion, immune escape, and therapeutic resistance. Therapeutic paradigms based on deconvoluting key molecular mechanisms driving gliomagenesis are urgently needed. Quaking (Qki, encoded by Qk) is frequently altered in GBM patients; Qk mutations or deletions occur in 35% percent of cases, and the Qki protein is absent in 50-60% of cases. Our lab has characterized Qki as important tumor suppressor in GBM, where deletion of Qk enables pre-malignant neural stem cells to expand outside their niche and develop into tumors that recapitulate human GBM. We discovered that Qki functions as a transcriptional coactivator of lipid metabolism genes, whereby Qki loss disrupts lipid homeostasis and compromises the integrity of various membrane structures. Several downstream processes governed by Qki have been delineated; however, upstream regulators of Qki have yet to be identified. Recurrent cancer mutations to specific Qki arginine sites implicate the dysregulation of arginine methylation, a common post-translational modification catalyzed by protein arginine methyltransferases (PRMTs). Leveraging in vitro methylation assays, we demonstrate that Qki is selectively methylated by the PRMT coactivator-associated arginine methyltransferase 1 (CARM1), specifically in the Quaking regulatory domain where cancer mutations are reported. We observe that Qki interacts with known CARM1 substrates, functioning in the transcriptional complex assembled by CARM1. Through mutagenesis studies, we identified arginine 242 (R242) and arginine 256 (R256) as specific CARM1-mediated methylation sites on Qki. Importantly, mutations to these sites compromise Qki’s activity as a transcriptional coactivator. Moreover, brain-specific deletion of CARM1 in vivo results in neurological phenotypes reminiscent of Qki deletion. Altogether, we provide evidence that CARM1 represents a novel tumor suppressor in GBM that functions through the arginine methylation of Qki.

EXTH-30. GENETIC ALTERATIONS THAT DEREGULATE RB AND PDGFRA SIGNALING PATHWAYS DRIVE TUMOR PROGRESSION IN IDH2-MUTANT ASTROCYTOMA

Abstract In IDH-mutant astrocytoma, IDH2 mutation is quite rare and biological mechanisms underlying tumor progression in IDH2-mutant astrocytoma remain unclear. In this presentation, we report a unique case of IDH2 mutant astrocytoma, CNS WHO grade 3 that developed tumor progression. We performed a comprehensive genomic and epigenomic analysis for primary and recurrent tumors and found that both tumors harbored recurrent IDH2R172K and TP53R248W mutation with CDKN2A/B hemizygous deletion. We also found amplifications of CDK4 and MDM2 with PDGFRA gain in the recur- rent tumor and upregulated protein expressions of these genes. We further developed, for the first time, a xenograft mouse model of IDH2R172K and TP53R248W mutant astrocytoma from the recurrent tumor, but not from the primary tumor. Consistent with parent recurrent tumor cells, amplifications of CDK4 and MDM2 and PDGFRA gain were found, while CDKN2A/B was identified as homozygous deletion in the xenografts, qualifying for integrated diagnosis of astro- cytoma, IDH2-mutant, CNS WHO grade 4. Cell viability assay found that CDK4/6 inhibitor and PDGFR inhibitor potently decreased cell viability in recurrent tumor cells, as compared to primary tumor cells. On the other hand, in accord with our previous study that IDH1 inhibitor was not sufficient to induce anti-tumor effects in IDH1-mutant high-grade gliomas (Tateishi K et al. Cancer Cell. 2015), we did not find decreased cell viability nor histone methylation status changes after mutation specific IDH2 inhibitor treatment of recurrent cells. These findings underlie that gene alterations that activate retinoblastoma (RB) signaling pathways and PDGFR may drive tumor progression and xenograft formation in IDH2-mutant astrocytoma, which is equivalent to progressive IDH1-mutant astrocytoma. Also, our findings suggest that these genomic alterations may represent therapeutic targets in IDH2-mutant astrocytoma.

PATH-05. CLINICAL, PATHOLOGICAL AND MOLECULAR DISEASE CHARACTERISTICS OF DIFFUSE HEMISPHERIC GLIOMA, H3 G34-MUTANT

Abstract BACKGROUND Diffuse hemispheric glioma, histone 3 (H3) G34-mutant, is a pediatric-type diffuse high-grade glioma newly defined in the World Health Organization (WHO) classification of central nervous system tumors 2021. Here we sought to define the prognostic roles of clinical, neuroimaging, pathological, and molecular features of these tumors. METHODS We retrospectively assembled a cohort of 114 patients with diffuse hemispheric glioma, H3 G34-mutant and profiled the imaging presentation and the molecular landscape of their tumors. RESULTS Compared with glioblastoma, H3 G34-mutant tumors exhibited less avid contrast enhancement, less necrosis and less edema on MRI. Comprehensive analyses of mutational and DNA copy number profiles revealed recurrent mutations in TP53 and ATRX, homozygous deletions of CDKN2A/B, and amplifications of PDGFRA, EGFR, CCND2, and MYCN. MGMT promoter methylation was detected in 79 tumors (75%); 11 tumors (13%) showed DNA copy number profiles suggestive of circumscribed deletions on 10q26.3 involving the MGMT locus. Median survival was 21.5 months (95% CI 15.3-27.7) and eight patients (7.0%) survived for ≥ five years. Female sex, gross total resection, and MGMT promoter methylation were positive prognostic factors on univariate analysis. Among radiological, pathological and molecular features, absence of pial invasion, and presence of microvascular proliferation and CDK6 amplification were positive prognostic factors on univariate analyses. CONCLUSION This study refines the clinical and molecular landscape of H3 G34-mutant diffuse hemispheric gliomas. Dedicated trials for this novel tumor type are urgently needed.

EPCO-21. ELUCIDATING THE FUNCTIONAL RELEVANCE OF ATRX-DEFICIENCY IN H3.3-G34-MUTANT DIFFUSE HEMISPHERIC GLIOMA

Abstract Diffuse hemispheric gliomas (DHGs) account for 30% of aggressive cerebral tumors in children and young adults, exhibiting abysmal outcomes. Co-existing recurrent mutations in H3.3 histones at residue G34 (H3.3-G34R/V mutation) and concurrent inactivating mutations in TP53 and α-thalassemia/intellectual disability-X-linked gene (ATRX) implicate a coordinated molecular effort to drive oncogenesis. ATRX, a core component of the SWItch/Sucrose Non-Fermentable chromatin remodeling complex, regulates the incorporation of histone H3.3 into chromatin sites across the genome to maintain epigenome integrity. Yet, it is unclear how ATRX loss combines with H3.3-G34R/V mutations to influence cellular phenotype and dysregulate neuro-developmental programs. We propose that ATRX deficiency coordinates with key oncogenic partners by inducing oncogenic transcriptional programs and neuro-developmental pathways in DHGs. To investigate this, we employed CRISPR-editing to model H3.3-G34R followed by ATRX knockdown (ATRX-KD) in a TP53 mutant (TP53-mut) human-induced pluripotent stem cell (h-iPSC) line, developing an isogenic system to map contributions to epigenetic dysfunction made by specific molecular alterations. Upon differentiation of our h-iPSCs to neural stem cells (NSCs), we found unique transcriptional profiles associated with each genetic alteration, with upregulation of forebrain progenitor genes driven by ATRX-loss. Hierarchal clustering of normalized transcript counts revealed gene signatures from each model driving unique functional pathways, with the ATRX-KD and the triple mutant (TP53-mut, ATRX-KD, H3.3-G34R) signatures enriched for neural development pathways. Additionally, both signatures were associated with published transcriptional profiles of G34-mutant DHGs, emphasizing the disease relevance of our models. Further, time-course analysis using cerebral organoids uncovered distinct morphological changes with each alteration, with the triple mutant exhibiting impaired differentiation at later time points. These latter findings suggest that ATRX deficiency transcriptionally influences early neuronal differentiation, effects further refined by H3.3-G34 mutation. To conclude, our innovative models demonstrate the involvement of ATRX in neuro-developmental and differentiation phenotypes, illuminating underlying molecular features of aggressive DHGs.

Clinicopathological Analysis of a European Cohort of MYOD1 Mutant Rhabdomyosarcomas in Children and Young Adults.

Patients with PAX3/7-FOXO1 fusion-negative rhabdomyosarcomas (fnRMS) harbouring the rare L122R MYOD1 mutation have significantly poorer prognosis than other fnRMS. We undertook a detailed clinicopathological evaluation of a cohort of patients with MYOD1 mutated fnRMS in order to improve risk stratification and treatment options. Histological, mutational and clinical data from a cohort of patients with MYOD1 mutant RMS treated in Europe were analysed. Thirty-two cases with mutant MYOD1 RMS were identified from patients enrolled in sequential European rhabdomyosarcoma clinical trials from 1992 to 2022 (n = 22) and non-trial cohorts (n = 10). Thirty cases had the recurrent L122R missense mutation, one case harboured a K124E mutation and one case had a truncating mutation (S63X). Increased MyoD1 and reduced MYF4 immunostaining were consistent features of MYOD1L122R-mutated RMS. Applying the risk stratification of the European paediatric Soft tissue sarcoma Study Group (EpSSG) RMS2005 trial, among 20 localised RMS cases that could be assigned a risk category, one was Very High Risk, 13 were High Risk and six were Standard Risk. Eight patients had distant metastases at diagnosis. Of the 25 patients with adequate clinical follow-up data, 15/25 (60%) patients had an event at a median time of 9months (12/15 included failure of local control) and 13/25 (52%) died of disease. This MYOD1 mutant cohort demonstrates increased MYOD and reduced MYF4 immunostaining, high risk of local failure and poor survival in agreement with other studies. Increased treatment intensity and improved local control should be considered for these patients.

Detection of Recurrent Mutations, Immunoglobulin Rearrangements and Copy Number Changes in Cell-Free DNA and Bone Marrow on Patients with Waldenstrom's Macroglobulinemia over a Course of Treatment

Detection of Recurrent Mutations, Immunoglobulin Rearrangements and Copy Number Changes in Cell-Free DNA and Bone Marrow on Patients with Waldenstrom's Macroglobulinemia over a Course of Treatment

Multiomic Single Cell Profiling Identifies Drivers of Progression in T-Cell Prolymphocytic Leukemia

Treatments for T-cell prolymphocytic leukemia (T-PLL), while transiently effective in the frontline, have failed to achieve any substantial improvement in the outcomes of this ultra-rare chronic leukemia. Patients with relapsed T-PLL have a dismal prognosis, with a median overall survival (OS) of less than 6 months. For this study we used samples collected from: 8 patients with untreated T-PLL, 2 with relapsed/refractory (R/R) T-PLL, and 1 from a PDX model of R/R T-PLL. Whole-exome sequencing (WES) was used to elucidate the mutational landscape and single cell T-cell receptor sequencing (scTCRseq), coupled with single cell RNA sequencing (scRNA-seq), was used to generate gene expression and TCR clonality signatures at the single cell level. The WES revealed a higher frequency of mutations in R/R T-PLL compared to their baseline counterparts. R/R T-PLL samples displayed mutations of CXCR4 (37%; p.S312fs), STAT5B (46%; p.N642H), ATM (82%; p.L2890V), SAMHD1 (92%; p.A565T) and BCOR (p.N1585fs) and deletions in ASXL2 which were absent in treatment naïve T-PLL. In addition, all T-PLL samples harbored recurrent mutations on CXCR4, CD27, JAK1, STAT3, CCND1, CDKN1B, and the epigenetic regulators KMT2C, KMT2B, TET2, and KDM5C. The mutational profiles revealed the genomic complexity of T-PLL. The ubiquitous presence of activating mutations affecting the JAK/STAT axis underscored their importance in driving T-PLL survival. We also studied the diversity of TCR clonality and its relationship with pathogenesis and prognosis in T-PLL. All the samples exhibited dominance of at least one to up to 3 specific CDR3 sequences, revealing the anticipated clonal expansion in T-PLL. Expression of TCRα and TCRβ genes in the dominant clone differed among the samples.Monoclonality was validated as biallelic only when the 2nd largest transcripts of CDR3α or CDR3β clones were at least 5 times larger than its subceeder. The coupled TCR seq and RNA seq analysis displayed varied degrees of clonal expansions at a single cell resolution across all the patient samples. The T cell subsets were characterized by the expression of various T cell-markers across the cell clusters. In particular, 60% of the samples showed more expression of IL7R and lesser expression CD8A and CD8B, indicating their ability in suppressing the antitumor immunity. CD3E and CD3D were highly expressed across the clusters of T-PLL datasets.Out of 11 datasets, NKG7 and GZMA (cytotoxic T cell markers) were identified in more than 40% of the samples. The augmented levels of anti-apoptosis (BCL-2) and Jak/Stat signaling (JAK1, STAT3) markers were seen across the clusters of T-PLL scRNA seq datasets. The higher expression of PPP1R14B was found in 70% of the samples indicating its probable role in poor prognosis in T-PLL. In conclusion, T-PLL is characterized by numerous genomic aberrations, presence of 1-3 dominant clones, and gene expression signatures that facilitate survival, and resistance to apoptosis.